From b99b90fdb53e2ef9ef4e9737e289456b3662699a Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Sun, 7 May 2023 00:14:20 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/recount3@da20bd4367b91f4196d716d81fa3700c59f95121=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- SUPPORT.html | 2 +- apple-touch-icon-120x120.png | Bin 2351 -> 2351 bytes apple-touch-icon-152x152.png | Bin 3002 -> 3002 bytes apple-touch-icon-180x180.png | Bin 3510 -> 3510 bytes apple-touch-icon-60x60.png | Bin 1811 -> 1811 bytes apple-touch-icon-76x76.png | Bin 1539 -> 1539 bytes apple-touch-icon.png | Bin 3510 -> 3510 bytes articles/index.html | 2 +- articles/recount3-quickstart.html | 126 +++++------ authors.html | 6 +- favicon-16x16.png | Bin 657 -> 657 bytes favicon-32x32.png | Bin 1156 -> 1156 bytes index.html | 2 +- news/index.html | 7 +- pkgdown.yml | 2 +- reference/annotation_ext.html | 2 +- reference/annotation_options.html | 2 +- reference/available_projects.html | 10 +- reference/available_samples.html | 10 +- reference/compute_read_counts.html | 48 ++--- reference/compute_scale_factors.html | 22 +- reference/create_hub.html | 16 +- reference/create_rse.html | 304 +++++++++++++-------------- reference/create_rse_manual.html | 76 +++---- reference/expand_sra_attributes.html | 30 +-- reference/file_retrieve.html | 28 +-- reference/index.html | 2 +- reference/is_paired_end.html | 22 +- reference/locate_url.html | 6 +- reference/locate_url_ann.html | 2 +- reference/project_homes.html | 2 +- reference/read_counts.html | 14 +- reference/read_metadata.html | 42 ++-- reference/recount3-package.html | 2 +- reference/recount3_cache.html | 2 +- reference/recount3_cache_files.html | 2 +- reference/recount3_cache_rm.html | 2 +- reference/transform_counts.html | 24 +-- 41 files changed, 414 insertions(+), 409 deletions(-) diff --git a/404.html b/404.html index 296cffd..93cbbd6 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ recount3 - 1.11.1 + 1.11.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index d35ef05..7aa5681 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ recount3 - 1.11.1 + 1.11.2 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 5735012..89db0d3 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ recount3 - 1.11.1 + 1.11.2 diff --git a/SUPPORT.html b/SUPPORT.html index a838240..e4e5bab 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ recount3 - 1.11.1 + 1.11.2 diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index ae0a98c2284da88dc95b678b5886b86424c38e28..9291757cb12c99f1aa7c11e62860a5faa8d8f58e 100644 GIT binary patch delta 68 zcmZ24v|eaJ6+1fvry@V++>MRD*hS1k3=FIcEUk=QN delta 68 zcmZ24v|eaJ6+4@_rlx80J41q}7z`)ADpt5#W?c{zASqupd1*LCK H=FSHIhNltU delta 68 zcmdlbzDs;U6+4@_rq-ISO&c3qxkSuDjEt>J46RIzv<(cb3=BM`HawUt#Vv~=VR^zL JX0kVTJ^;r<6Pf@3 diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 447ed9af6f6a00433db077086e64fafbb6005b1d..c2a3620d1dad2c5a20d8f6cf30733c488f1893f0 100644 GIT binary patch delta 92 zcmdlcy-j*T6+1fvr}9JgKN}kxd0fpy3=FIcEUk=9wLuJnYo>cYGcYiymbgZgq$HN4 gTIJ@aWTsUz7#SED>l&Eq8lY=fp26xr*_}5Z02|>NtpET3 delta 92 zcmdlcy-j*T6+4@_ruOaLrj3n_Jg#OTM#feqhE^uV+6D$z1_tjQb%!u8FsPQeMwFx^ imZVzc=BH$)RWcYE7#ZstnCcp!YnZ>^_{C&*-h2QzM;rM7 diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index d20d909655b25b61673c7e4c916752e36ba9c682..8ec9becee34406357e13a1dc621143abb60b802e 100644 GIT binary patch delta 95 zcmbQtH<@ok01F2@1E>7CjE47{BUsp(T+Kra46F<+t&9z|K@0<>s+kWM7#LJbTq8vPVVBUsp(T+Kp^jIB%zt&A?DmGBYqRsFt`! ll%ync8S5ID>KdSHFyu&asZhbUc4Ol?7FY8S0|P4qODkg|Z4kpicv5pM0|SF gRc?MtW?ChKk%5u1u7Rnp0lJ2y^VSC^Phrgm0FcZXtpET3 delta 92 zcmZqXY37+w#m*+Kso~Ued1K=_7FV+nBV#KQLn{*lZ36=<1B3fq6HhWQFsPQeMwFx^ imZVzc=BH$)RWcYE7#ZstnCcp!YgiYqSvq+NYd!$vE*fJ1 diff --git a/apple-touch-icon.png b/apple-touch-icon.png index 16b3ecea4f63c86058ed85999d0f1953b140bad6..d14a9660d9d3f9696e0a52e3f3d5f54d34c6c58e 100644 GIT binary patch delta 92 zcmdlcy-j*T6+1fvr%HWt=ElZG9#``a0|P4qODkhDZ4krY`Q7Dt3=9maC9V-ADTyVi gR=N2pnQ4^_Mg~U4x(24Y2Iv~5HOOC@?9Q7H0QcY;*#H0l delta 92 zcmdlcy-j*T6+4@_rjF}N@r{j*Jg#OTM#feqhE^sf+6D$z1_s)$TW>KiFsPQeMwFx^ imZVzc=BH$)RWcYE7#ZstnCcp!YlxEIO`Gh_n-2idei;)0 diff --git a/articles/index.html b/articles/index.html index 897d65f..b239ae6 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ recount3 - 1.11.1 + 1.11.2 diff --git a/articles/recount3-quickstart.html b/articles/recount3-quickstart.html index 061d6c7..b7cbc4f 100644 --- a/articles/recount3-quickstart.html +++ b/articles/recount3-quickstart.html @@ -41,7 +41,7 @@ recount3 - 1.11.1 + 1.11.2 @@ -95,7 +95,7 @@

Leonardo University
-

6 May 2023

+

7 May 2023

Source: vignettes/recount3-quickstart.Rmd @@ -215,7 +215,7 @@

Citing #> project_. doi:10.18129/B9.bioc.recount3 #> <https://doi.org/10.18129/B9.bioc.recount3>, #> https://github.com/LieberInstitute/recount3 - R package version -#> 1.11.1, <http://www.bioconductor.org/packages/recount3>. +#> 1.11.2, <http://www.bioconductor.org/packages/recount3>. #> #> Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, #> Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, @@ -250,9 +250,9 @@

Quick start
 ## Find all available human projects
 human_projects <- available_projects()
-#> 2023-05-06 23:44:50.223282 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:44:50.469118 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:44:50.659536 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:13:09.092849 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:13:09.470188 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:13:09.797249 caching file tcga.recount_project.MD.gz.
 
 ## Find the project you are interested in,
 ## here we use SRP009615 as an example
@@ -263,17 +263,17 @@ 
Quick start## Create a RangedSummarizedExperiment (RSE) object at the gene level
 rse_gene_SRP009615 <- create_rse(proj_info)
-#> 2023-05-06 23:44:55.82056 downloading and reading the metadata.
-#> 2023-05-06 23:44:55.994663 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:44:56.213808 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:44:56.426054 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:56.640289 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:56.851982 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:44:56.9342 downloading and reading the feature information.
-#> 2023-05-06 23:44:57.08476 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:44:57.615091 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:44:57.776566 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:44:58.030335 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:13:14.229616 downloading and reading the metadata.
+#> 2023-05-07 00:13:14.522375 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:13:14.84609 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:13:15.174247 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:15.538286 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:15.860603 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:13:15.935994 downloading and reading the feature information.
+#> 2023-05-07 00:13:16.213029 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:13:16.729389 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:13:17.001371 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:13:17.224353 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore that RSE object
 rse_gene_SRP009615
@@ -521,9 +521,9 @@ 
Through available_projects()
 
 human_projects <- available_projects()
-#> 2023-05-06 23:44:58.803888 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:44:58.987009 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:44:59.173614 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:13:18.06864 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:13:18.377585 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:13:18.705197 caching file tcga.recount_project.MD.gz.
 dim(human_projects)
 #> [1] 8742    6
 head(human_projects)
@@ -709,17 +709,17 @@ 
Build a RSE
 ## Create a RSE object at the gene level
 rse_gene_SRP009615 <- create_rse(project_info)
-#> 2023-05-06 23:45:03.378364 downloading and reading the metadata.
-#> 2023-05-06 23:45:03.517137 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:45:03.698916 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:45:03.887932 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:04.071244 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:04.259634 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:45:04.344924 downloading and reading the feature information.
-#> 2023-05-06 23:45:04.470372 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:45:04.997401 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:45:05.123315 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:45:05.355473 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:13:22.336787 downloading and reading the metadata.
+#> 2023-05-07 00:13:22.630779 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:13:22.940676 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:13:23.257932 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:23.599902 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:23.932979 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:13:24.009546 downloading and reading the feature information.
+#> 2023-05-07 00:13:24.293872 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:13:24.802968 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:13:25.067825 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:13:25.275564 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE gene object
 rse_gene_SRP009615
@@ -747,13 +747,13 @@ 
Explore the RSE## Information about how this RSE object was made
 metadata(rse_gene_SRP009615)
 #> $time_created
-#> [1] "2023-05-06 23:45:05 UTC"
+#> [1] "2023-05-07 00:13:25 UTC"
 #> 
 #> $recount3_version
 #>           package ondiskversion loadedversion                        path
-#> recount3 recount3        1.11.1        1.11.1 /__w/_temp/Library/recount3
+#> recount3 recount3        1.11.2        1.11.2 /__w/_temp/Library/recount3
 #>                           loadedpath attached is_base       date       source
-#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-06 Bioconductor
+#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-07 Bioconductor
 #>          md5ok            library
 #> recount3    NA /__w/_temp/Library
 #> 
@@ -980,17 +980,17 @@ 
Exon
     proj_info,
     type = "exon"
 )
-#> 2023-05-06 23:45:06.172741 downloading and reading the metadata.
-#> 2023-05-06 23:45:06.315896 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:45:06.501451 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:45:06.693027 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:06.890256 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:07.119364 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:45:07.202948 downloading and reading the feature information.
-#> 2023-05-06 23:45:07.358249 caching file human.exon_sums.G026.gtf.gz.
-#> 2023-05-06 23:45:30.915382 downloading and reading the counts: 12 samples across 1299686 features.
-#> 2023-05-06 23:45:31.178964 caching file sra.exon_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:45:33.719337 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:13:26.019767 downloading and reading the metadata.
+#> 2023-05-07 00:13:26.340216 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:13:26.653524 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:13:26.964942 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:27.292065 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:27.606952 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:13:27.682036 downloading and reading the feature information.
+#> 2023-05-07 00:13:27.9505 caching file human.exon_sums.G026.gtf.gz.
+#> 2023-05-07 00:13:50.074768 downloading and reading the counts: 12 samples across 1299686 features.
+#> 2023-05-07 00:13:50.66939 caching file sra.exon_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:13:52.96192 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE exon object
 rse_exon_SRP009615
@@ -1171,19 +1171,19 @@ 
Exon-exon junctionsproj_info,
     type = "jxn"
 )
-#> 2023-05-06 23:45:39.743301 downloading and reading the metadata.
-#> 2023-05-06 23:45:39.99523 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:45:40.175934 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:45:40.391297 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:40.582871 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:45:40.774463 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:45:40.857767 downloading and reading the feature information.
-#> 2023-05-06 23:45:41.01147 caching file sra.junctions.SRP009615.ALL.RR.gz.
-#> 2023-05-06 23:45:42.898738 downloading and reading the counts: 12 samples across 281448 features.
-#> 2023-05-06 23:45:43.073241 caching file sra.junctions.SRP009615.ALL.MM.gz.
-#> 2023-05-06 23:45:43.704555 matching exon-exon junction counts with the metadata.
-#> 2023-05-06 23:45:43.836062 caching file sra.junctions.SRP009615.ALL.ID.gz.
-#> 2023-05-06 23:45:43.979101 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:13:58.486701 downloading and reading the metadata.
+#> 2023-05-07 00:13:59.030464 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:13:59.331674 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:13:59.625764 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:13:59.947766 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:14:00.270782 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:14:00.346054 downloading and reading the feature information.
+#> 2023-05-07 00:14:00.611637 caching file sra.junctions.SRP009615.ALL.RR.gz.
+#> 2023-05-07 00:14:02.320374 downloading and reading the counts: 12 samples across 281448 features.
+#> 2023-05-07 00:14:02.580696 caching file sra.junctions.SRP009615.ALL.MM.gz.
+#> 2023-05-07 00:14:03.190086 matching exon-exon junction counts with the metadata.
+#> 2023-05-07 00:14:03.457154 caching file sra.junctions.SRP009615.ALL.ID.gz.
+#> 2023-05-07 00:14:03.589659 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE exon-exon junctions object
 rse_jxn_SRP009615
@@ -1593,9 +1593,9 @@ 
Reproducibilityfile.remove("quickstartRef.bib")
 #> [1] TRUE

 
Date the vignette was generated.

-
#> [1] "2023-05-06 23:45:46 UTC"

+
#> [1] "2023-05-07 00:14:05 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 1.115 mins

+
#> Time difference of 1.124 mins

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1607,7 +1607,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2023-05-06
+#>  date     2023-05-07
 #>  pandoc   2.19.2 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1682,7 +1682,7 @@ 
Reproducibility#>  ragg                   1.2.5     2023-01-12 [2] RSPM (R 4.3.0)
 #>  Rcpp                   1.0.10    2023-01-22 [2] RSPM (R 4.3.0)
 #>  RCurl                  1.98-1.12 2023-03-27 [1] RSPM (R 4.3.0)
-#>  recount3             * 1.11.1    2023-05-06 [1] Bioconductor
+#>  recount3             * 1.11.2    2023-05-07 [1] Bioconductor
 #>  RefManageR             1.4.0     2022-09-30 [1] CRAN (R 4.3.0)
 #>  restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.3.0)
 #>  rjson                  0.2.21    2022-01-09 [1] CRAN (R 4.3.0)
@@ -1746,7 +1746,7 @@ 
Bibliographyhttps://github.com/cboettig/knitcitations.

 
[6] L. Collado-Torres. Explore and download data from the
 recount3 project. https://github.com/LieberInstitute/recount3 - R package
-version 1.11.1. 2023. DOI: 10.18129/B9.bioc.recount3. http://www.bioconductor.org/packages/recount3.

+version 1.11.2. 2023. DOI: 10.18129/B9.bioc.recount3. http://www.bioconductor.org/packages/recount3.

 
[7] L. Collado-Torres, A. Nellore, and A. E. Jaffe. “recount
 workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
 [version 1; referees: 1 approved, 2 approved with reservations]”. In:
diff --git a/authors.html b/authors.html
index 1ad17d8..263c147 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -73,14 +73,14 @@ 
Citation

 
     
Collado-Torres L (2023).
 Explore and download data from the recount3 project.
-doi:10.18129/B9.bioc.recount3, https://github.com/LieberInstitute/recount3 - R package version 1.11.1, http://www.bioconductor.org/packages/recount3. 
+doi:10.18129/B9.bioc.recount3, https://github.com/LieberInstitute/recount3 - R package version 1.11.2, http://www.bioconductor.org/packages/recount3. 
 

     
@Manual{,
   title = {Explore and download data from the recount3 project},
   author = {Leonardo Collado-Torres},
   year = {2023},
   url = {http://www.bioconductor.org/packages/recount3},
-  note = {https://github.com/LieberInstitute/recount3 - R package version 1.11.1},
+  note = {https://github.com/LieberInstitute/recount3 - R package version 1.11.2},
   doi = {10.18129/B9.bioc.recount3},
 }

     
Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B (2021).
diff --git a/favicon-16x16.png b/favicon-16x16.png
index 8be406a7b651f760c4544eef03f04998e6017d72..5686e61abc41c05c0672d1b9c5eaa488567da33c 100644
GIT binary patch
delta 70
zcmbQpI+1ll0wV`I1E(hACDF3U8H}YO<{<_KRtA<V3=FCzt`Q|E
ji6yC4x%nxXX_X8{21drZ2Bx|O=o&J(jBZR8WyuEs^gJ1T

delta 95
zcmZqSY~kE+l!=2)T+{f(Ln*t>XPKB8UCly_jIB%ztxOHI4GgRd47OgM^_YQyLAAs+
lq9i4;B-JW6KP5A*lEKKp$XM6FRM!Aq!;vnf_{pLy`2a!98#n*}

diff --git a/index.html b/index.html
index d640a6a..9efa32f 100644
--- a/index.html
+++ b/index.html
@@ -45,7 +45,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/news/index.html b/news/index.html
index e1a767a..197dc11 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -57,6 +57,11 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+
recount3 1.11.2

+
SIGNIFICANT USER-VISIBLE CHANGES

+

     

 
recount3 1.11.1

 
SIGNIFICANT USER-VISIBLE CHANGES

diff --git a/pkgdown.yml b/pkgdown.yml
index 38ee011..852a299 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   recount3-quickstart: recount3-quickstart.html
-last_built: 2023-05-06T23:41Z
+last_built: 2023-05-07T00:09Z
 
diff --git a/reference/annotation_ext.html b/reference/annotation_ext.html
index d5d2e12..5670302 100644
--- a/reference/annotation_ext.html
+++ b/reference/annotation_ext.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
diff --git a/reference/annotation_options.html b/reference/annotation_options.html
index 0a25df2..42334cd 100644
--- a/reference/annotation_options.html
+++ b/reference/annotation_options.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/available_projects.html b/reference/available_projects.html
index 011d681..e2e0f99 100644
--- a/reference/available_projects.html
+++ b/reference/available_projects.html
@@ -17,7 +17,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -117,9 +117,9 @@ 
Examples

     

 ## Find all the human projects
 human_projects <- available_projects()
-#> 2023-05-06 23:42:11.90205 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:42:12.150847 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:42:12.385882 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:10:05.710375 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:06.059883 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:10:06.403144 caching file tcga.recount_project.MD.gz.
 
 ## Explore the results
 dim(human_projects)
@@ -175,7 +175,7 @@ 
Examples

 
 ## Find all the mouse projects
 mouse_projects <- available_projects(organism = "mouse")
-#> 2023-05-06 23:42:18.377642 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:12.289013 caching file sra.recount_project.MD.gz.
 
 ## Explore the results
 dim(mouse_projects)
diff --git a/reference/available_samples.html b/reference/available_samples.html
index 92f4611..2889a81 100644
--- a/reference/available_samples.html
+++ b/reference/available_samples.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -128,9 +128,9 @@ 
Examples

     

 ## Find all the human samples available from recount3
 human_samples <- available_samples()
-#> 2023-05-06 23:42:22.881495 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:42:23.069531 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:42:23.271649 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:10:16.352644 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:16.658074 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:10:17.013503 caching file tcga.recount_project.MD.gz.
 dim(human_samples)
 #> [1] 347005      7
 head(human_samples)
@@ -165,7 +165,7 @@ 
Examples

 
 ## Find all the mouse samples available from recount3
 mouse_samples <- available_samples("mouse")
-#> 2023-05-06 23:42:25.62861 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:19.163851 caching file sra.recount_project.MD.gz.
 dim(mouse_samples)
 #> [1] 416859      7
 head(mouse_samples)
diff --git a/reference/compute_read_counts.html b/reference/compute_read_counts.html
index cd5bdf2..141ef39 100644
--- a/reference/compute_read_counts.html
+++ b/reference/compute_read_counts.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -128,17 +128,17 @@ 
Examples

     

 ## Create a RSE object at the gene level
 rse_gene_SRP009615 <- create_rse_manual("SRP009615")
-#> 2023-05-06 23:42:29.049371 downloading and reading the metadata.
-#> 2023-05-06 23:42:29.20305 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:42:29.394682 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:42:29.587938 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:29.822555 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:30.020602 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:42:30.109075 downloading and reading the feature information.
-#> 2023-05-06 23:42:30.250785 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:42:30.818995 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:42:30.951706 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:42:31.236552 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:22.027918 downloading and reading the metadata.
+#> 2023-05-07 00:10:22.332659 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:10:22.640917 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:10:22.966372 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:23.315081 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:23.628464 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:10:23.704635 downloading and reading the feature information.
+#> 2023-05-07 00:10:23.983416 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:10:24.519525 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:10:24.830053 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:10:25.069605 constructing the RangedSummarizedExperiment (rse) object.
 colSums(compute_read_counts(rse_gene_SRP009615)) / 1e6
 #> SRR387777 SRR387778 SRR387779 SRR387780 SRR389079 SRR389080 SRR389081 SRR389082 
 #>  21.29962  23.66484  32.62525  25.46085  41.48717  28.05485  17.78092  15.46669 
@@ -147,17 +147,17 @@ 
Examples

 
 ## Create a RSE object at the gene level
 rse_gene_DRP000499 <- create_rse_manual("DRP000499")
-#> 2023-05-06 23:42:31.322323 downloading and reading the metadata.
-#> 2023-05-06 23:42:31.485876 caching file sra.sra.DRP000499.MD.gz.
-#> 2023-05-06 23:42:31.728159 caching file sra.recount_project.DRP000499.MD.gz.
-#> 2023-05-06 23:42:31.951636 caching file sra.recount_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:42:32.142234 caching file sra.recount_seq_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:42:32.364365 caching file sra.recount_pred.DRP000499.MD.gz.
-#> 2023-05-06 23:42:32.449278 downloading and reading the feature information.
-#> 2023-05-06 23:42:32.583311 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:42:33.080178 downloading and reading the counts: 21 samples across 63856 features.
-#> 2023-05-06 23:42:33.273949 caching file sra.gene_sums.DRP000499.G026.gz.
-#> 2023-05-06 23:42:33.54724 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:25.147308 downloading and reading the metadata.
+#> 2023-05-07 00:10:25.417019 caching file sra.sra.DRP000499.MD.gz.
+#> 2023-05-07 00:10:25.734304 caching file sra.recount_project.DRP000499.MD.gz.
+#> 2023-05-07 00:10:26.051436 caching file sra.recount_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:10:26.365882 caching file sra.recount_seq_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:10:26.72776 caching file sra.recount_pred.DRP000499.MD.gz.
+#> 2023-05-07 00:10:26.803488 downloading and reading the feature information.
+#> 2023-05-07 00:10:27.079844 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:10:27.552718 downloading and reading the counts: 21 samples across 63856 features.
+#> 2023-05-07 00:10:27.855395 caching file sra.gene_sums.DRP000499.G026.gz.
+#> 2023-05-07 00:10:28.09871 constructing the RangedSummarizedExperiment (rse) object.
 colSums(compute_read_counts(rse_gene_DRP000499)) / 1e6
 #> DRR001622 DRR001623 DRR001624 DRR001625 DRR001626 DRR001627 DRR001628 DRR001629 
 #> 10.952140  7.995718 11.874082       NaN  7.518984 11.272031 53.412769 27.539984 
@@ -186,7 +186,7 @@ 
Examples

 
 ## Repeat for DRP000499, a paired-end study
 recount::download_study("DRP000499", outdir = tempdir())
-#> 2023-05-06 23:42:37.887298 downloading file rse_gene.Rdata to /tmp/Rtmp225BAB
+#> 2023-05-07 00:10:31.92353 downloading file rse_gene.Rdata to /tmp/RtmpAxQcvh
 load(file.path(tempdir(), "rse_gene.Rdata"), verbose = TRUE)
 #> Loading objects:
 #>   rse_gene
diff --git a/reference/compute_scale_factors.html b/reference/compute_scale_factors.html
index 4b847b2..dd07bb2 100644
--- a/reference/compute_scale_factors.html
+++ b/reference/compute_scale_factors.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -157,11 +157,11 @@ 
Examples

         )
     )
 )
-#> 2023-05-06 23:42:40.543723 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:42:40.747118 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:42:40.940678 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:41.148005 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:41.350407 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:10:35.994636 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:10:36.306626 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:10:36.62662 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:36.949452 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:37.28351 caching file sra.recount_pred.SRP009615.MD.gz.
 
 ## Compute the scaling factors
 compute_scale_factors(SRP009615_meta, by = "auc")
@@ -184,11 +184,11 @@ 
Examples

         )
     )
 )
-#> 2023-05-06 23:42:41.592596 caching file sra.sra.DRP000499.MD.gz.
-#> 2023-05-06 23:42:41.835978 caching file sra.recount_project.DRP000499.MD.gz.
-#> 2023-05-06 23:42:42.03765 caching file sra.recount_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:42:42.254452 caching file sra.recount_seq_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:42:42.468868 caching file sra.recount_pred.DRP000499.MD.gz.
+#> 2023-05-07 00:10:37.655073 caching file sra.sra.DRP000499.MD.gz.
+#> 2023-05-07 00:10:37.981805 caching file sra.recount_project.DRP000499.MD.gz.
+#> 2023-05-07 00:10:38.304785 caching file sra.recount_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:10:38.635387 caching file sra.recount_seq_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:10:38.999166 caching file sra.recount_pred.DRP000499.MD.gz.
 
 ## Compute the scaling factors
 compute_scale_factors(DRP000499_meta, by = "auc")
diff --git a/reference/create_hub.html b/reference/create_hub.html
index 9bfa00c..c757b1e 100644
--- a/reference/create_hub.html
+++ b/reference/create_hub.html
@@ -21,7 +21,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -154,7 +154,7 @@ 
Examples

     

 ## Find all the mouse samples available from recount3
 mouse_samples <- available_samples("mouse")
-#> 2023-05-06 23:42:43.1134 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:39.698728 caching file sra.recount_project.MD.gz.
 
 ## Subset to project DRP001299
 info_DRP001299 <- subset(mouse_samples, project == "DRP001299")
@@ -164,9 +164,9 @@ 
Examples

 ## List the files created by create_hub()
 hub_files <- list.files(hub_dir, full.names = TRUE, recursive = TRUE)
 hub_files
-#> [1] "/tmp/Rtmp225BAB/DRP001299/genomes.txt"     
-#> [2] "/tmp/Rtmp225BAB/DRP001299/hub.txt"         
-#> [3] "/tmp/Rtmp225BAB/DRP001299/mm10/trackDb.txt"
+#> [1] "/tmp/RtmpAxQcvh/DRP001299/genomes.txt"     
+#> [2] "/tmp/RtmpAxQcvh/DRP001299/hub.txt"         
+#> [3] "/tmp/RtmpAxQcvh/DRP001299/mm10/trackDb.txt"
 
 ## Check the files contents
 sapply(hub_files, function(x) {
@@ -259,13 +259,13 @@ 
Examples

 #> type bigWig
 #> visibility hide
 #> autoScale on
-#> $`/tmp/Rtmp225BAB/DRP001299/genomes.txt`
+#> $`/tmp/RtmpAxQcvh/DRP001299/genomes.txt`
 #> NULL
 #> 
-#> $`/tmp/Rtmp225BAB/DRP001299/hub.txt`
+#> $`/tmp/RtmpAxQcvh/DRP001299/hub.txt`
 #> NULL
 #> 
-#> $`/tmp/Rtmp225BAB/DRP001299/mm10/trackDb.txt`
+#> $`/tmp/RtmpAxQcvh/DRP001299/mm10/trackDb.txt`
 #> NULL
 #> 
 
diff --git a/reference/create_rse.html b/reference/create_rse.html
index 355b8b9..cd37771 100644
--- a/reference/create_rse.html
+++ b/reference/create_rse.html
@@ -21,7 +21,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -145,9 +145,9 @@ 
Examples

     

 ## Find all available human projects
 human_projects <- available_projects()
-#> 2023-05-06 23:42:47.03038 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:42:47.22355 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:42:47.42453 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:10:43.158444 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:10:43.471854 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:10:43.842242 caching file tcga.recount_project.MD.gz.
 
 ## Find the project you are interested in
 proj_info <- subset(
@@ -157,17 +157,17 @@ 
Examples

 
 ## Create a RSE object at the gene level
 rse_gene_SRP009615 <- create_rse(proj_info)
-#> 2023-05-06 23:42:51.887481 downloading and reading the metadata.
-#> 2023-05-06 23:42:52.02409 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:42:52.234165 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:42:52.423363 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:52.615222 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:52.814323 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:42:52.906368 downloading and reading the feature information.
-#> 2023-05-06 23:42:53.020535 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:42:53.530814 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:42:53.660784 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:42:53.864296 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:47.629258 downloading and reading the metadata.
+#> 2023-05-07 00:10:47.93515 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:10:48.253151 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:10:48.573828 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:48.891872 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:49.203151 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:10:49.285469 downloading and reading the feature information.
+#> 2023-05-07 00:10:49.557602 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:10:50.043949 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:10:50.311859 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:10:50.493249 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE gene object
 rse_gene_SRP009615
@@ -185,13 +185,13 @@ 
Examples

 ## Information about how this RSE object was made
 metadata(rse_gene_SRP009615)
 #> $time_created
-#> [1] "2023-05-06 23:42:53 UTC"
+#> [1] "2023-05-07 00:10:50 UTC"
 #> 
 #> $recount3_version
 #>           package ondiskversion loadedversion                        path
-#> recount3 recount3        1.11.1        1.11.1 /__w/_temp/Library/recount3
+#> recount3 recount3        1.11.2        1.11.2 /__w/_temp/Library/recount3
 #>                           loadedpath attached is_base       date       source
-#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-06 Bioconductor
+#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-07 Bioconductor
 #>          md5ok            library
 #> recount3    NA /__w/_temp/Library
 #> 
@@ -526,17 +526,17 @@ 
Examples

     proj_info,
     annotation = "fantom6_cat"
 )
-#> 2023-05-06 23:42:56.429709 downloading and reading the metadata.
-#> 2023-05-06 23:42:56.569936 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:42:56.793318 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:42:56.9974 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:57.217247 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:57.427985 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:42:57.5236 downloading and reading the feature information.
-#> 2023-05-06 23:42:57.670089 caching file human.gene_sums.F006.gtf.gz.
-#> 2023-05-06 23:42:58.135068 downloading and reading the counts: 12 samples across 124047 features.
-#> 2023-05-06 23:42:58.295091 caching file sra.gene_sums.SRP009615.F006.gz.
-#> 2023-05-06 23:42:58.62447 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:53.784254 downloading and reading the metadata.
+#> 2023-05-07 00:10:54.069448 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:10:54.378223 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:10:54.715142 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:55.034494 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:55.34915 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:10:55.432427 downloading and reading the feature information.
+#> 2023-05-07 00:10:55.710198 caching file human.gene_sums.F006.gtf.gz.
+#> 2023-05-07 00:10:56.156776 downloading and reading the counts: 12 samples across 124047 features.
+#> 2023-05-07 00:10:56.42205 caching file sra.gene_sums.SRP009615.F006.gz.
+#> 2023-05-07 00:10:56.708977 constructing the RangedSummarizedExperiment (rse) object.
 rowRanges(rse_gene_SRP009615_fantom6_cat)
 #> GRanges object with 124047 ranges and 5 metadata columns:
 #>                   seqnames            ranges strand |   source     type
@@ -573,17 +573,17 @@ 
Examples

     proj_info,
     annotation = "refseq"
 )
-#> 2023-05-06 23:42:58.667087 downloading and reading the metadata.
-#> 2023-05-06 23:42:58.832634 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:42:59.020973 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:42:59.219508 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:59.424344 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:42:59.627602 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:42:59.721697 downloading and reading the feature information.
-#> 2023-05-06 23:42:59.870372 caching file human.gene_sums.R109.gtf.gz.
-#> 2023-05-06 23:43:00.443989 downloading and reading the counts: 12 samples across 54042 features.
-#> 2023-05-06 23:43:00.592456 caching file sra.gene_sums.SRP009615.R109.gz.
-#> 2023-05-06 23:43:00.870184 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:56.746102 downloading and reading the metadata.
+#> 2023-05-07 00:10:57.029173 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:10:57.349174 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:10:57.664051 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:57.98792 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:10:58.3011 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:10:58.384231 downloading and reading the feature information.
+#> 2023-05-07 00:10:58.64316 caching file human.gene_sums.R109.gtf.gz.
+#> 2023-05-07 00:10:59.200787 downloading and reading the counts: 12 samples across 54042 features.
+#> 2023-05-07 00:10:59.469325 caching file sra.gene_sums.SRP009615.R109.gz.
+#> 2023-05-07 00:10:59.701913 constructing the RangedSummarizedExperiment (rse) object.
 rowRanges(rse_gene_SRP009615_refseq)
 #> GRanges object with 54042 ranges and 25 metadata columns:
 #>               seqnames            ranges strand |   source     type bp_length
@@ -685,17 +685,17 @@ 
Examples

     proj_info,
     annotation = "ercc"
 )
-#> 2023-05-06 23:43:00.909608 downloading and reading the metadata.
-#> 2023-05-06 23:43:01.061015 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:01.266932 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:01.488942 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:01.692079 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:01.970371 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:02.066833 downloading and reading the feature information.
-#> 2023-05-06 23:43:02.205717 caching file human.gene_sums.ERCC.gtf.gz.
-#> 2023-05-06 23:43:02.303559 downloading and reading the counts: 12 samples across 92 features.
-#> 2023-05-06 23:43:02.42531 caching file sra.gene_sums.SRP009615.ERCC.gz.
-#> 2023-05-06 23:43:02.554152 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:10:59.736376 downloading and reading the metadata.
+#> 2023-05-07 00:11:00.02302 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:00.345005 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:00.66956 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:01.031001 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:01.36341 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:01.447554 downloading and reading the feature information.
+#> 2023-05-07 00:11:01.718114 caching file human.gene_sums.ERCC.gtf.gz.
+#> 2023-05-07 00:11:01.803771 downloading and reading the counts: 12 samples across 92 features.
+#> 2023-05-07 00:11:02.067252 caching file sra.gene_sums.SRP009615.ERCC.gz.
+#> 2023-05-07 00:11:02.17908 constructing the RangedSummarizedExperiment (rse) object.
 rowRanges(rse_gene_SRP009615_ercc)
 #> GRanges object with 92 ranges and 6 metadata columns:
 #>                seqnames    ranges strand |   source     type bp_length
@@ -732,17 +732,17 @@ 
Examples

     proj_info,
     annotation = "sirv"
 )
-#> 2023-05-06 23:43:02.591313 downloading and reading the metadata.
-#> 2023-05-06 23:43:02.734847 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:02.991617 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:03.202506 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:03.416243 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:03.633025 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:03.748039 downloading and reading the feature information.
-#> 2023-05-06 23:43:03.910417 caching file human.gene_sums.SIRV.gtf.gz.
-#> 2023-05-06 23:43:04.026095 downloading and reading the counts: 12 samples across 7 features.
-#> 2023-05-06 23:43:04.177542 caching file sra.gene_sums.SRP009615.SIRV.gz.
-#> 2023-05-06 23:43:04.549338 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:02.211417 downloading and reading the metadata.
+#> 2023-05-07 00:11:02.497324 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:02.886448 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:03.22362 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:03.557758 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:03.889899 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:03.989911 downloading and reading the feature information.
+#> 2023-05-07 00:11:04.287838 caching file human.gene_sums.SIRV.gtf.gz.
+#> 2023-05-07 00:11:04.387151 downloading and reading the counts: 12 samples across 7 features.
+#> 2023-05-07 00:11:04.643488 caching file sra.gene_sums.SRP009615.SIRV.gz.
+#> 2023-05-07 00:11:04.946357 constructing the RangedSummarizedExperiment (rse) object.
 rowRanges(rse_gene_SRP009615_sirv)
 #> GRanges object with 7 ranges and 5 metadata columns:
 #>         seqnames      ranges strand |          source     type bp_length
@@ -770,72 +770,72 @@ 
Examples

 rses_gene <- lapply(annotation_options(), function(x) {
     create_rse(proj_info, type = "gene", annotation = x)
 })
-#> 2023-05-06 23:43:04.580292 downloading and reading the metadata.
-#> 2023-05-06 23:43:04.716582 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:04.903763 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:05.100328 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:05.323347 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:05.529651 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:05.624105 downloading and reading the feature information.
-#> 2023-05-06 23:43:05.751056 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:43:06.249622 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:43:06.375535 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:43:06.578255 constructing the RangedSummarizedExperiment (rse) object.
-#> 2023-05-06 23:43:06.604098 downloading and reading the metadata.
-#> 2023-05-06 23:43:06.762699 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:06.989179 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:07.202631 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:07.419839 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:07.63905 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:07.755053 downloading and reading the feature information.
-#> 2023-05-06 23:43:07.877758 caching file human.gene_sums.G029.gtf.gz.
-#> 2023-05-06 23:43:08.488818 downloading and reading the counts: 12 samples across 64837 features.
-#> 2023-05-06 23:43:08.649024 caching file sra.gene_sums.SRP009615.G029.gz.
-#> 2023-05-06 23:43:08.833431 constructing the RangedSummarizedExperiment (rse) object.
-#> 2023-05-06 23:43:08.859304 downloading and reading the metadata.
-#> 2023-05-06 23:43:08.994055 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:09.190083 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:09.402148 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:09.604611 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:09.807163 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:09.903543 downloading and reading the feature information.
-#> 2023-05-06 23:43:10.033854 caching file human.gene_sums.F006.gtf.gz.
-#> 2023-05-06 23:43:10.48721 downloading and reading the counts: 12 samples across 124047 features.
-#> 2023-05-06 23:43:10.617164 caching file sra.gene_sums.SRP009615.F006.gz.
-#> 2023-05-06 23:43:10.954113 constructing the RangedSummarizedExperiment (rse) object.
-#> 2023-05-06 23:43:10.980035 downloading and reading the metadata.
-#> 2023-05-06 23:43:11.13815 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:11.317812 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:11.512074 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:11.711863 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:11.92662 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:12.018975 downloading and reading the feature information.
-#> 2023-05-06 23:43:12.14568 caching file human.gene_sums.R109.gtf.gz.
-#> 2023-05-06 23:43:12.828801 downloading and reading the counts: 12 samples across 54042 features.
-#> 2023-05-06 23:43:12.975954 caching file sra.gene_sums.SRP009615.R109.gz.
-#> 2023-05-06 23:43:14.148004 constructing the RangedSummarizedExperiment (rse) object.
-#> 2023-05-06 23:43:14.174717 downloading and reading the metadata.
-#> 2023-05-06 23:43:14.338204 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:14.521142 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:14.744647 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:14.941505 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:15.134014 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:15.225784 downloading and reading the feature information.
-#> 2023-05-06 23:43:15.363298 caching file human.gene_sums.ERCC.gtf.gz.
-#> 2023-05-06 23:43:15.456944 downloading and reading the counts: 12 samples across 92 features.
-#> 2023-05-06 23:43:15.59487 caching file sra.gene_sums.SRP009615.ERCC.gz.
-#> 2023-05-06 23:43:15.720579 constructing the RangedSummarizedExperiment (rse) object.
-#> 2023-05-06 23:43:15.744944 downloading and reading the metadata.
-#> 2023-05-06 23:43:15.891029 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:16.092915 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:16.298556 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:16.513518 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:16.725986 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:16.834973 downloading and reading the feature information.
-#> 2023-05-06 23:43:16.945366 caching file human.gene_sums.SIRV.gtf.gz.
-#> 2023-05-06 23:43:17.061675 downloading and reading the counts: 12 samples across 7 features.
-#> 2023-05-06 23:43:17.190997 caching file sra.gene_sums.SRP009615.SIRV.gz.
-#> 2023-05-06 23:43:17.335689 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:04.97308 downloading and reading the metadata.
+#> 2023-05-07 00:11:05.255507 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:05.573472 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:05.896726 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:06.22352 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:06.543992 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:06.627071 downloading and reading the feature information.
+#> 2023-05-07 00:11:06.926447 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:11:07.418048 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:11:07.680464 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:11:07.860845 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:07.883122 downloading and reading the metadata.
+#> 2023-05-07 00:11:08.16528 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:08.493349 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:08.861712 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:09.19383 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:09.52885 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:09.628582 downloading and reading the feature information.
+#> 2023-05-07 00:11:09.9042 caching file human.gene_sums.G029.gtf.gz.
+#> 2023-05-07 00:11:10.480122 downloading and reading the counts: 12 samples across 64837 features.
+#> 2023-05-07 00:11:10.747085 caching file sra.gene_sums.SRP009615.G029.gz.
+#> 2023-05-07 00:11:10.916615 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:10.938466 downloading and reading the metadata.
+#> 2023-05-07 00:11:11.207739 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:11.582081 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:11.901201 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:12.224091 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:12.547452 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:12.632961 downloading and reading the feature information.
+#> 2023-05-07 00:11:12.899991 caching file human.gene_sums.F006.gtf.gz.
+#> 2023-05-07 00:11:13.338635 downloading and reading the counts: 12 samples across 124047 features.
+#> 2023-05-07 00:11:13.593051 caching file sra.gene_sums.SRP009615.F006.gz.
+#> 2023-05-07 00:11:13.889259 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:13.911845 downloading and reading the metadata.
+#> 2023-05-07 00:11:14.172178 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:14.515338 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:14.835939 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:15.157787 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:15.477671 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:15.559414 downloading and reading the feature information.
+#> 2023-05-07 00:11:15.816875 caching file human.gene_sums.R109.gtf.gz.
+#> 2023-05-07 00:11:16.457783 downloading and reading the counts: 12 samples across 54042 features.
+#> 2023-05-07 00:11:16.690823 caching file sra.gene_sums.SRP009615.R109.gz.
+#> 2023-05-07 00:11:17.646302 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:17.669385 downloading and reading the metadata.
+#> 2023-05-07 00:11:17.956727 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:18.259673 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:18.570068 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:18.891008 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:19.211854 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:19.293309 downloading and reading the feature information.
+#> 2023-05-07 00:11:19.545496 caching file human.gene_sums.ERCC.gtf.gz.
+#> 2023-05-07 00:11:19.628367 downloading and reading the counts: 12 samples across 92 features.
+#> 2023-05-07 00:11:19.884436 caching file sra.gene_sums.SRP009615.ERCC.gz.
+#> 2023-05-07 00:11:19.993551 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:20.01458 downloading and reading the metadata.
+#> 2023-05-07 00:11:20.29704 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:20.619707 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:20.955975 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:21.296625 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:21.632452 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:21.729379 downloading and reading the feature information.
+#> 2023-05-07 00:11:21.986019 caching file human.gene_sums.SIRV.gtf.gz.
+#> 2023-05-07 00:11:22.084423 downloading and reading the counts: 12 samples across 7 features.
+#> 2023-05-07 00:11:22.335658 caching file sra.gene_sums.SRP009615.SIRV.gz.
+#> 2023-05-07 00:11:22.462359 constructing the RangedSummarizedExperiment (rse) object.
 names(rses_gene) <- annotation_options()
 rses_gene
 #> $gencode_v26
@@ -913,17 +913,17 @@ 
Examples

     proj_info,
     type = "exon"
 )
-#> 2023-05-06 23:43:17.456648 downloading and reading the metadata.
-#> 2023-05-06 23:43:17.615353 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:17.837465 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:18.193804 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:18.425927 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:18.667885 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:18.795694 downloading and reading the feature information.
-#> 2023-05-06 23:43:18.926553 caching file human.exon_sums.G026.gtf.gz.
-#> 2023-05-06 23:43:42.810024 downloading and reading the counts: 12 samples across 1299686 features.
-#> 2023-05-06 23:43:43.043085 caching file sra.exon_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:43:44.42 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:22.566979 downloading and reading the metadata.
+#> 2023-05-07 00:11:22.849387 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:23.19788 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:23.833256 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:24.190655 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:24.621315 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:24.734605 downloading and reading the feature information.
+#> 2023-05-07 00:11:25.016062 caching file human.exon_sums.G026.gtf.gz.
+#> 2023-05-07 00:11:46.831422 downloading and reading the counts: 12 samples across 1299686 features.
+#> 2023-05-07 00:11:47.362236 caching file sra.exon_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:11:48.649303 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE exon object
 rse_exon_SRP009615
@@ -1069,19 +1069,19 @@ 
Examples

     proj_info,
     type = "jxn"
 )
-#> 2023-05-06 23:43:48.968843 downloading and reading the metadata.
-#> 2023-05-06 23:43:49.218132 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:49.418124 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:49.618649 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:49.819233 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:50.033696 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:50.127803 downloading and reading the feature information.
-#> 2023-05-06 23:43:50.253749 caching file sra.junctions.SRP009615.ALL.RR.gz.
-#> 2023-05-06 23:43:52.2031 downloading and reading the counts: 12 samples across 281448 features.
-#> 2023-05-06 23:43:52.33146 caching file sra.junctions.SRP009615.ALL.MM.gz.
-#> 2023-05-06 23:43:53.248641 matching exon-exon junction counts with the metadata.
-#> 2023-05-06 23:43:53.386882 caching file sra.junctions.SRP009615.ALL.ID.gz.
-#> 2023-05-06 23:43:53.502011 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:11:52.826972 downloading and reading the metadata.
+#> 2023-05-07 00:11:53.116512 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:11:53.423539 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:11:53.746409 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:54.072303 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:11:54.386513 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:11:54.471267 downloading and reading the feature information.
+#> 2023-05-07 00:11:54.790385 caching file sra.junctions.SRP009615.ALL.RR.gz.
+#> 2023-05-07 00:11:56.49752 downloading and reading the counts: 12 samples across 281448 features.
+#> 2023-05-07 00:11:56.796275 caching file sra.junctions.SRP009615.ALL.MM.gz.
+#> 2023-05-07 00:11:57.576621 matching exon-exon junction counts with the metadata.
+#> 2023-05-07 00:11:57.838492 caching file sra.junctions.SRP009615.ALL.ID.gz.
+#> 2023-05-07 00:11:57.941144 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Explore the resulting RSE exon-exon junctions object
 rse_jxn_SRP009615
diff --git a/reference/create_rse_manual.html b/reference/create_rse_manual.html
index b715ef0..8d827fd 100644
--- a/reference/create_rse_manual.html
+++ b/reference/create_rse_manual.html
@@ -20,7 +20,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -173,17 +173,17 @@ 
Examples

     "SRP009615",
     "data_sources/sra"
 )
-#> 2023-05-06 23:43:56.081234 downloading and reading the metadata.
-#> 2023-05-06 23:43:56.2317 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:43:56.438292 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:43:56.637406 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:56.838457 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:43:57.034173 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:43:57.441103 downloading and reading the feature information.
-#> 2023-05-06 23:43:57.584768 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:43:58.074906 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:43:58.222507 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:43:58.401081 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:12:00.557621 downloading and reading the metadata.
+#> 2023-05-07 00:12:00.848869 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:12:01.193886 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:12:01.510686 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:01.833772 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:02.15607 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:12:02.477324 downloading and reading the feature information.
+#> 2023-05-07 00:12:02.745714 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:12:03.220237 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:12:03.489067 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:03.656085 constructing the RangedSummarizedExperiment (rse) object.
 rse_gene_SRP009615_manual
 #> class: RangedSummarizedExperiment 
 #> dim: 63856 12 
@@ -208,19 +208,19 @@ 
Examples

     "collections/geuvadis_smartseq",
     recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
 )
-#> 2023-05-06 23:43:58.54771 downloading and reading the metadata.
-#> 2023-05-06 23:43:58.740328 caching file geuvadis_smartseq.recount_project.gz.
-#> 2023-05-06 23:43:58.844435 caching file sra.sra.ERP110066.MD.gz.
-#> 2023-05-06 23:43:58.936969 caching file sra.recount_project.ERP110066.MD.gz.
-#> 2023-05-06 23:43:59.034626 caching file sra.recount_qc.ERP110066.MD.gz.
+#> 2023-05-07 00:12:03.785307 downloading and reading the metadata.
+#> 2023-05-07 00:12:04.265943 caching file geuvadis_smartseq.recount_project.gz.
+#> 2023-05-07 00:12:04.466651 caching file sra.sra.ERP110066.MD.gz.
+#> 2023-05-07 00:12:04.657549 caching file sra.recount_project.ERP110066.MD.gz.
+#> 2023-05-07 00:12:04.85334 caching file sra.recount_qc.ERP110066.MD.gz.
 #> Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available.
-#> 2023-05-06 23:43:59.159735 caching file sra.recount_pred.ERP110066.MD.gz.
-#> 2023-05-06 23:43:59.261156 caching file geuvadis_smartseq.custom.gz.
-#> 2023-05-06 23:43:59.564211 downloading and reading the feature information.
-#> 2023-05-06 23:43:59.591634 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:44:00.118188 downloading and reading the counts: 1 sample across 63856 features.
-#> 2023-05-06 23:44:00.145744 caching file sra.gene_sums.ERP110066.G026.gz.
-#> 2023-05-06 23:44:02.620963 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:12:05.179351 caching file sra.recount_pred.ERP110066.MD.gz.
+#> 2023-05-07 00:12:05.378524 caching file geuvadis_smartseq.custom.gz.
+#> 2023-05-07 00:12:05.648144 downloading and reading the feature information.
+#> 2023-05-07 00:12:05.778548 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:12:06.283255 downloading and reading the counts: 1 sample across 63856 features.
+#> 2023-05-07 00:12:06.413842 caching file sra.gene_sums.ERP110066.G026.gz.
+#> 2023-05-07 00:12:08.762478 constructing the RangedSummarizedExperiment (rse) object.
 rse_gene_ERP110066_collection_manual
 #> class: RangedSummarizedExperiment 
 #> dim: 63856 1 
@@ -243,17 +243,17 @@ 
Examples

     "data_sources/sra",
     organism = "mouse"
 )
-#> 2023-05-06 23:44:02.767445 downloading and reading the metadata.
-#> 2023-05-06 23:44:03.41801 caching file sra.sra.DRP002367.MD.gz.
-#> 2023-05-06 23:44:03.630164 caching file sra.recount_project.DRP002367.MD.gz.
-#> 2023-05-06 23:44:03.848559 caching file sra.recount_qc.DRP002367.MD.gz.
-#> 2023-05-06 23:44:04.078264 caching file sra.recount_seq_qc.DRP002367.MD.gz.
-#> 2023-05-06 23:44:04.309397 caching file sra.recount_pred.DRP002367.MD.gz.
-#> 2023-05-06 23:44:04.400879 downloading and reading the feature information.
-#> 2023-05-06 23:44:04.554811 caching file mouse.gene_sums.M023.gtf.gz.
-#> 2023-05-06 23:44:06.641292 downloading and reading the counts: 4 samples across 55421 features.
-#> 2023-05-06 23:44:06.775444 caching file sra.gene_sums.DRP002367.M023.gz.
-#> 2023-05-06 23:44:06.914767 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:12:08.888969 downloading and reading the metadata.
+#> 2023-05-07 00:12:14.578888 caching file sra.sra.DRP002367.MD.gz.
+#> 2023-05-07 00:12:14.93374 caching file sra.recount_project.DRP002367.MD.gz.
+#> 2023-05-07 00:12:15.297514 caching file sra.recount_qc.DRP002367.MD.gz.
+#> 2023-05-07 00:12:15.615882 caching file sra.recount_seq_qc.DRP002367.MD.gz.
+#> 2023-05-07 00:12:15.936019 caching file sra.recount_pred.DRP002367.MD.gz.
+#> 2023-05-07 00:12:16.016256 downloading and reading the feature information.
+#> 2023-05-07 00:12:16.279003 caching file mouse.gene_sums.M023.gtf.gz.
+#> 2023-05-07 00:12:18.000451 downloading and reading the counts: 4 samples across 55421 features.
+#> 2023-05-07 00:12:18.284909 caching file sra.gene_sums.DRP002367.M023.gz.
+#> 2023-05-07 00:12:18.411522 constructing the RangedSummarizedExperiment (rse) object.
 rse_gene_DRP002367_manual
 #> class: RangedSummarizedExperiment 
 #> dim: 55421 4 
@@ -269,13 +269,13 @@ 
Examples

 ## Information about how this RSE was made
 metadata(rse_gene_DRP002367_manual)
 #> $time_created
-#> [1] "2023-05-06 23:44:06 UTC"
+#> [1] "2023-05-07 00:12:18 UTC"
 #> 
 #> $recount3_version
 #>           package ondiskversion loadedversion                        path
-#> recount3 recount3        1.11.1        1.11.1 /__w/_temp/Library/recount3
+#> recount3 recount3        1.11.2        1.11.2 /__w/_temp/Library/recount3
 #>                           loadedpath attached is_base       date       source
-#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-06 Bioconductor
+#> recount3 /__w/_temp/Library/recount3     TRUE   FALSE 2023-05-07 Bioconductor
 #>          md5ok            library
 #> recount3    NA /__w/_temp/Library
 #> 
diff --git a/reference/expand_sra_attributes.html b/reference/expand_sra_attributes.html
index 1ad5165..fa86f44 100644
--- a/reference/expand_sra_attributes.html
+++ b/reference/expand_sra_attributes.html
@@ -20,7 +20,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -106,9 +106,9 @@ 
Examples

     

 ## Find all available human projects
 human_projects <- available_projects()
-#> 2023-05-06 23:44:07.410991 caching file sra.recount_project.MD.gz.
-#> 2023-05-06 23:44:07.615296 caching file gtex.recount_project.MD.gz.
-#> 2023-05-06 23:44:07.834003 caching file tcga.recount_project.MD.gz.
+#> 2023-05-07 00:12:18.971639 caching file sra.recount_project.MD.gz.
+#> 2023-05-07 00:12:19.291246 caching file gtex.recount_project.MD.gz.
+#> 2023-05-07 00:12:19.631356 caching file tcga.recount_project.MD.gz.
 
 ## Find the project you are interested in
 proj_info <- subset(
@@ -118,17 +118,17 @@ 
Examples

 
 ## Create a RSE object at the gene level
 rse_gene_SRP009615 <- create_rse(proj_info)
-#> 2023-05-06 23:44:10.379648 downloading and reading the metadata.
-#> 2023-05-06 23:44:10.558891 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:44:10.776064 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:44:10.994375 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:11.213025 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:11.430257 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:44:11.523191 downloading and reading the feature information.
-#> 2023-05-06 23:44:11.683657 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:44:12.199557 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:44:12.343862 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:44:12.537379 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:12:21.845299 downloading and reading the metadata.
+#> 2023-05-07 00:12:22.180084 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:12:22.496025 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:12:22.814289 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:23.151212 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:23.475999 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:12:23.558369 downloading and reading the feature information.
+#> 2023-05-07 00:12:23.841686 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:12:24.337531 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:12:24.608303 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:24.787148 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Expand the SRA attributes (see details for more information)
 rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)
diff --git a/reference/file_retrieve.html b/reference/file_retrieve.html
index ef82495..3f858a8 100644
--- a/reference/file_retrieve.html
+++ b/reference/file_retrieve.html
@@ -17,7 +17,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     

 
@@ -118,22 +118,22 @@ 
Examples

 local_SRP009615_meta <- file_retrieve(
     url = url_SRP009615_meta
 )
-#> 2023-05-06 23:44:13.068503 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:44:13.275893 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:44:13.473902 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:13.676564 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:13.870554 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:12:25.437357 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:12:25.749973 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:12:26.070817 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:26.409835 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:26.724754 caching file sra.recount_pred.SRP009615.MD.gz.
 local_SRP009615_meta
 #>                                                           sra.sra.SRP009615.MD.gz 
-#>              "/github/home/.cache/R/recount3/2246947efba_sra.sra.SRP009615.MD.gz" 
+#>             "/github/home/.cache/R/recount3/22486fd6f29d_sra.sra.SRP009615.MD.gz" 
 #>                                               sra.recount_project.SRP009615.MD.gz 
-#> "/github/home/.cache/R/recount3/22462823556d_sra.recount_project.SRP009615.MD.gz" 
+#> "/github/home/.cache/R/recount3/2248613da13d_sra.recount_project.SRP009615.MD.gz" 
 #>                                                    sra.recount_qc.SRP009615.MD.gz 
-#>       "/github/home/.cache/R/recount3/22468a12a26_sra.recount_qc.SRP009615.MD.gz" 
+#>      "/github/home/.cache/R/recount3/2248638ef0e5_sra.recount_qc.SRP009615.MD.gz" 
 #>                                                sra.recount_seq_qc.SRP009615.MD.gz 
-#>  "/github/home/.cache/R/recount3/2246679b42d6_sra.recount_seq_qc.SRP009615.MD.gz" 
+#>  "/github/home/.cache/R/recount3/2248157b9e27_sra.recount_seq_qc.SRP009615.MD.gz" 
 #>                                                  sra.recount_pred.SRP009615.MD.gz 
-#>    "/github/home/.cache/R/recount3/224618b6b209_sra.recount_pred.SRP009615.MD.gz" 
+#>     "/github/home/.cache/R/recount3/22487841d23_sra.recount_pred.SRP009615.MD.gz" 
 
 ## Download the gene counts file for project SRP009615
 url_SRP009615_gene <- locate_url(
@@ -144,10 +144,10 @@ 
Examples

 local_SRP009615_gene <- file_retrieve(
     url = url_SRP009615_gene
 )
-#> 2023-05-06 23:44:14.092788 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:27.071847 caching file sra.gene_sums.SRP009615.G026.gz.
 local_SRP009615_gene
-#>                                               sra.gene_sums.SRP009615.G026.gz 
-#> "/github/home/.cache/R/recount3/224655b8d058_sra.gene_sums.SRP009615.G026.gz" 
+#>                                              sra.gene_sums.SRP009615.G026.gz 
+#> "/github/home/.cache/R/recount3/224837bbd78_sra.gene_sums.SRP009615.G026.gz" 
 

     
   
diff --git a/reference/index.html b/reference/index.html
index d4f3e40..8592571 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/is_paired_end.html b/reference/is_paired_end.html
index a64877f..860d93f 100644
--- a/reference/is_paired_end.html
+++ b/reference/is_paired_end.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -119,11 +119,11 @@ 
Examples

         )
     )
 )
-#> 2023-05-06 23:44:14.478877 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:44:14.676168 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:44:14.879494 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:15.097134 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:15.316719 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:12:27.585102 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:12:27.907695 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:12:28.24191 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:28.579797 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:28.912438 caching file sra.recount_pred.SRP009615.MD.gz.
 
 ## Are the samples paired end?
 is_paired_end(SRP009615_meta)
@@ -141,11 +141,11 @@ 
Examples

         )
     )
 )
-#> 2023-05-06 23:44:15.573859 caching file sra.sra.DRP000499.MD.gz.
-#> 2023-05-06 23:44:15.84979 caching file sra.recount_project.DRP000499.MD.gz.
-#> 2023-05-06 23:44:16.10485 caching file sra.recount_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:44:16.358314 caching file sra.recount_seq_qc.DRP000499.MD.gz.
-#> 2023-05-06 23:44:16.599522 caching file sra.recount_pred.DRP000499.MD.gz.
+#> 2023-05-07 00:12:29.291998 caching file sra.sra.DRP000499.MD.gz.
+#> 2023-05-07 00:12:29.636309 caching file sra.recount_project.DRP000499.MD.gz.
+#> 2023-05-07 00:12:29.984132 caching file sra.recount_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:12:30.343642 caching file sra.recount_seq_qc.DRP000499.MD.gz.
+#> 2023-05-07 00:12:30.707121 caching file sra.recount_pred.DRP000499.MD.gz.
 is_paired_end(DRP000499_meta)
 #> Warning: is_paired_end(): Looks like some samples failed to align and will return NA.
 #> DRR001622 DRR001623 DRR001624 DRR001625 DRR001626 DRR001627 DRR001628 DRR001629 
diff --git a/reference/locate_url.html b/reference/locate_url.html
index 204cc1e..36d05fd 100644
--- a/reference/locate_url.html
+++ b/reference/locate_url.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -172,7 +172,7 @@ 
Examples

     "collections/geuvadis_smartseq",
     recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
 )
-#> 2023-05-06 23:44:17.208948 caching file geuvadis_smartseq.recount_project.gz.
+#> 2023-05-07 00:12:31.505758 caching file geuvadis_smartseq.recount_project.gz.
 #>                                                                                                          sra.sra.ERP110066.MD.gz 
 #>             "http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.sra.ERP110066.MD.gz" 
 #>                                                                                              sra.recount_project.ERP110066.MD.gz 
@@ -221,7 +221,7 @@ 
Examples

     "gene",
     recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
 )
-#> 2023-05-06 23:44:17.313327 caching file geuvadis_smartseq.recount_project.gz.
+#> 2023-05-07 00:12:31.703993 caching file geuvadis_smartseq.recount_project.gz.
 #>                                                                                               sra.gene_sums.ERP110066.G026.gz 
 #> "http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/gene_sums/66/ERP110066/sra.gene_sums.ERP110066.G026.gz" 
 
diff --git a/reference/locate_url_ann.html b/reference/locate_url_ann.html
index c2688f4..4aae477 100644
--- a/reference/locate_url_ann.html
+++ b/reference/locate_url_ann.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/project_homes.html b/reference/project_homes.html
index 78ef41e..68e6255 100644
--- a/reference/project_homes.html
+++ b/reference/project_homes.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/read_counts.html b/reference/read_counts.html
index 14ae5a8..7d24d8f 100644
--- a/reference/read_counts.html
+++ b/reference/read_counts.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -116,12 +116,12 @@ 
Examples

     type = "gene"
 )
 local_SRP009615_gene <- file_retrieve(url = url_SRP009615_gene)
-#> 2023-05-06 23:44:18.349147 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:32.972618 caching file sra.gene_sums.SRP009615.G026.gz.
 
 ## Read the gene counts, take about 3 seconds
 system.time(SRP009615_gene_counts <- read_counts(local_SRP009615_gene))
 #>    user  system elapsed 
-#>   0.111   0.004   0.115 
+#>   0.103   0.004   0.106 
 dim(SRP009615_gene_counts)
 #> [1] 63856    12
 
@@ -168,10 +168,10 @@ 
Examples

         type = "exon"
     )
 )
-#> 2023-05-06 23:44:19.87027 caching file sra.exon_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:34.394238 caching file sra.exon_sums.SRP009615.G026.gz.
 local_SRP009615_exon
-#>                                               sra.exon_sums.SRP009615.G026.gz 
-#> "/github/home/.cache/R/recount3/22465b399dff_sra.exon_sums.SRP009615.G026.gz" 
+#>                                              sra.exon_sums.SRP009615.G026.gz 
+#> "/github/home/.cache/R/recount3/2248fa92647_sra.exon_sums.SRP009615.G026.gz" 
 
 ## Read the exon counts, takes about 50-60 seconds
 system.time(
@@ -180,7 +180,7 @@ 
Examples

     )
 )
 #>    user  system elapsed 
-#>   0.947   0.112   1.060 
+#>   0.929   0.104   1.033 
 dim(SRP009615_exon_counts)
 #> [1] 1299686      12
 pryr::object_size(SRP009615_exon_counts)
diff --git a/reference/read_metadata.html b/reference/read_metadata.html
index 2454765..34e8269 100644
--- a/reference/read_metadata.html
+++ b/reference/read_metadata.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -107,11 +107,11 @@ 
Examples

 local_ERP110066_meta <- file_retrieve(
     url = url_ERP110066_meta
 )
-#> 2023-05-06 23:44:28.549226 caching file sra.sra.ERP110066.MD.gz.
-#> 2023-05-06 23:44:28.744756 caching file sra.recount_project.ERP110066.MD.gz.
-#> 2023-05-06 23:44:28.945605 caching file sra.recount_qc.ERP110066.MD.gz.
-#> 2023-05-06 23:44:29.18888 caching file sra.recount_seq_qc.ERP110066.MD.gz.
-#> 2023-05-06 23:44:29.41393 caching file sra.recount_pred.ERP110066.MD.gz.
+#> 2023-05-07 00:12:41.356664 caching file sra.sra.ERP110066.MD.gz.
+#> 2023-05-07 00:12:41.680826 caching file sra.recount_project.ERP110066.MD.gz.
+#> 2023-05-07 00:12:42.002532 caching file sra.recount_qc.ERP110066.MD.gz.
+#> 2023-05-07 00:12:42.338177 caching file sra.recount_seq_qc.ERP110066.MD.gz.
+#> 2023-05-07 00:12:42.665478 caching file sra.recount_pred.ERP110066.MD.gz.
 
 ## Read the metadata
 ERP110066_meta <- read_metadata(local_ERP110066_meta)
@@ -305,13 +305,13 @@ 
Examples

         )
     )
 )
-#> 2023-05-06 23:44:29.854212 caching file geuvadis_smartseq.recount_project.gz.
-#> 2023-05-06 23:44:29.966421 caching file sra.sra.ERP110066.MD.gz.
-#> 2023-05-06 23:44:30.065409 caching file sra.recount_project.ERP110066.MD.gz.
-#> 2023-05-06 23:44:30.169194 caching file sra.recount_qc.ERP110066.MD.gz.
+#> 2023-05-07 00:12:43.328535 caching file geuvadis_smartseq.recount_project.gz.
+#> 2023-05-07 00:12:43.531988 caching file sra.sra.ERP110066.MD.gz.
+#> 2023-05-07 00:12:43.724762 caching file sra.recount_project.ERP110066.MD.gz.
+#> 2023-05-07 00:12:43.920917 caching file sra.recount_qc.ERP110066.MD.gz.
 #> Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available.
-#> 2023-05-06 23:44:30.299108 caching file sra.recount_pred.ERP110066.MD.gz.
-#> 2023-05-06 23:44:30.406464 caching file geuvadis_smartseq.custom.gz.
+#> 2023-05-07 00:12:44.247336 caching file sra.recount_pred.ERP110066.MD.gz.
+#> 2023-05-07 00:12:44.448955 caching file geuvadis_smartseq.custom.gz.
 dim(ERP110066_collection_meta)
 #> [1]   1 161
 ## New columns for this collection
@@ -324,11 +324,11 @@ 
Examples

         locate_url("DRP002367", "data_sources/sra", organism = "mouse")
     )
 )
-#> 2023-05-06 23:44:31.09195 caching file sra.sra.DRP002367.MD.gz.
-#> 2023-05-06 23:44:31.339063 caching file sra.recount_project.DRP002367.MD.gz.
-#> 2023-05-06 23:44:31.563686 caching file sra.recount_qc.DRP002367.MD.gz.
-#> 2023-05-06 23:44:31.78786 caching file sra.recount_seq_qc.DRP002367.MD.gz.
-#> 2023-05-06 23:44:32.009327 caching file sra.recount_pred.DRP002367.MD.gz.
+#> 2023-05-07 00:12:45.597233 caching file sra.sra.DRP002367.MD.gz.
+#> 2023-05-07 00:12:46.163738 caching file sra.recount_project.DRP002367.MD.gz.
+#> 2023-05-07 00:12:46.506557 caching file sra.recount_qc.DRP002367.MD.gz.
+#> 2023-05-07 00:12:47.069095 caching file sra.recount_seq_qc.DRP002367.MD.gz.
+#> 2023-05-07 00:12:47.62098 caching file sra.recount_pred.DRP002367.MD.gz.
 dim(DRP002367_meta)
 #> [1]   4 176
 
@@ -338,10 +338,10 @@ 
Examples

         locate_url("BLADDER", "data_sources/gtex")
     )
 )
-#> 2023-05-06 23:44:32.306062 caching file gtex.gtex.BLADDER.MD.gz.
-#> 2023-05-06 23:44:32.542283 caching file gtex.recount_project.BLADDER.MD.gz.
-#> 2023-05-06 23:44:32.781844 caching file gtex.recount_qc.BLADDER.MD.gz.
-#> 2023-05-06 23:44:33.044199 caching file gtex.recount_seq_qc.BLADDER.MD.gz.
+#> 2023-05-07 00:12:48.21889 caching file gtex.gtex.BLADDER.MD.gz.
+#> 2023-05-07 00:12:48.850269 caching file gtex.recount_project.BLADDER.MD.gz.
+#> 2023-05-07 00:12:49.43457 caching file gtex.recount_qc.BLADDER.MD.gz.
+#> 2023-05-07 00:12:50.005816 caching file gtex.recount_seq_qc.BLADDER.MD.gz.
 
 dim(gtex_bladder_meta)
 #> [1]  21 197
diff --git a/reference/recount3-package.html b/reference/recount3-package.html
index c9cdf08..649434d 100644
--- a/reference/recount3-package.html
+++ b/reference/recount3-package.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/recount3_cache.html b/reference/recount3_cache.html
index dcbd763..116adf1 100644
--- a/reference/recount3_cache.html
+++ b/reference/recount3_cache.html
@@ -19,7 +19,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/recount3_cache_files.html b/reference/recount3_cache_files.html
index 805a680..c4a05d4 100644
--- a/reference/recount3_cache_files.html
+++ b/reference/recount3_cache_files.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/recount3_cache_rm.html b/reference/recount3_cache_rm.html
index b3f421c..3c5ffd4 100644
--- a/reference/recount3_cache_rm.html
+++ b/reference/recount3_cache_rm.html
@@ -18,7 +18,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
diff --git a/reference/transform_counts.html b/reference/transform_counts.html
index 8c1f16e..fa0c54b 100644
--- a/reference/transform_counts.html
+++ b/reference/transform_counts.html
@@ -28,7 +28,7 @@
       
       
         recount3
-        1.11.1
+        1.11.2
       
     
 
@@ -156,17 +156,17 @@ 
Examples

     

 ## Create a RSE object at the gene level
 rse_gene_SRP009615 <- create_rse_manual("SRP009615")
-#> 2023-05-06 23:44:34.551628 downloading and reading the metadata.
-#> 2023-05-06 23:44:34.687165 caching file sra.sra.SRP009615.MD.gz.
-#> 2023-05-06 23:44:35.066714 caching file sra.recount_project.SRP009615.MD.gz.
-#> 2023-05-06 23:44:35.266991 caching file sra.recount_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:35.481853 caching file sra.recount_seq_qc.SRP009615.MD.gz.
-#> 2023-05-06 23:44:35.690667 caching file sra.recount_pred.SRP009615.MD.gz.
-#> 2023-05-06 23:44:35.788755 downloading and reading the feature information.
-#> 2023-05-06 23:44:35.914631 caching file human.gene_sums.G026.gtf.gz.
-#> 2023-05-06 23:44:36.441705 downloading and reading the counts: 12 samples across 63856 features.
-#> 2023-05-06 23:44:36.569496 caching file sra.gene_sums.SRP009615.G026.gz.
-#> 2023-05-06 23:44:36.771128 constructing the RangedSummarizedExperiment (rse) object.
+#> 2023-05-07 00:12:51.616844 downloading and reading the metadata.
+#> 2023-05-07 00:12:52.103045 caching file sra.sra.SRP009615.MD.gz.
+#> 2023-05-07 00:12:52.699716 caching file sra.recount_project.SRP009615.MD.gz.
+#> 2023-05-07 00:12:53.047657 caching file sra.recount_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:53.58639 caching file sra.recount_seq_qc.SRP009615.MD.gz.
+#> 2023-05-07 00:12:54.127138 caching file sra.recount_pred.SRP009615.MD.gz.
+#> 2023-05-07 00:12:54.213777 downloading and reading the feature information.
+#> 2023-05-07 00:12:54.685976 caching file human.gene_sums.G026.gtf.gz.
+#> 2023-05-07 00:12:55.198254 downloading and reading the counts: 12 samples across 63856 features.
+#> 2023-05-07 00:12:55.680187 caching file sra.gene_sums.SRP009615.G026.gz.
+#> 2023-05-07 00:12:55.865277 constructing the RangedSummarizedExperiment (rse) object.
 
 ## Scale the counts using the AUC
 assays(rse_gene_SRP009615)$counts <- transform_counts(rse_gene_SRP009615)